Chamois (Rupicapra spp.) are medium-sized ungulates that inhabit alpine pastures and rocky areas on the main mountain massifs of both Europe and the Near East and, exceptionally, the low elevations of river gorges, forested and coastal areas. The currently accepted taxonomy of chamois, based on morphological, behavioral and molecular evidence, recognizes two species: the Northern chamois (Rupicapra rupicapra) with seven subspecies distributed on the Alps (R. r. rupicapra and R. r. cartusiana), the Balkans (R. r. balcanica), the Tatras (R. r. tatrica) and the Carpathians (R. r. carpatica), in western Asia (R. r. asiatica) and the Caucasus (R. r. caucasica). The Southern chamois (Rupicapra pyrenaica) includes three geographically isolated subspecies on the Cantabrian Massif (R. p. parva), the Pyrenees (R. p. pyrenaica) and the central Apennines (R. p. ornata). In the early 1900s, chamois populations in the northern Dinaric Mountains in Croatia were extirpated due to predation, natural events, and unsustainable hunting before their taxonomic classification was assessed. Several decades after local extinction, the chamois population was re-established through several reintroduction efforts between 1964 and 1978. This resulted in the current populations of Northern chamois in the northern Dinaric Mountains being descended from successfully reintroduced individuals, captured in mountainous areas in Bosnia and Herzegovina (Rupicapra r. balcanica) and Slovenia (Rupicapra r. rupicapra), except for the Dinara massif, where the only Croatian autochthonous population of Balkan chamois lives. Since different subspecies have been involved in reintroduction in the past, a contact zone has formed in the northern Velebit Mountains, where these subspecies hybridize. The Balkan chamois is widespread on the Balkan Peninsula, along mountain massifs from Croatia in the north to Greece in the south and Bulgaria in the east. The distribution of the Balkan chamois is patchy and covers only parts of the massifs and mountain chains across the countries that form its range. The subspecies has low rates of colonization and reduced gene flow between isolated populations, which may result in genetic differentiation due to the inbreeding effect and a loss of allelic variants as a consequence of genetic drift. Reduced genetic diversity in these small and isolated populations might, in turn, cause negative impacts on fitness, resulting in decreased effective population size and, eventually, increase the probabilities of extinction. Other threats to the Balkan chamois survival are considered to be poaching, introductions of other chamois subspecies (mostly Alpine chamois), forest succession, road infrastructure, intensive livestock grazing, predation, unsustainable hunting and natural events. Due to these threats, the Balkan chamois is protected by Annexes II and IV of the European Union Habitats Directive 92/43/EEC (OJ L 206, 22.7.1992) and Appendix III of the Bern Convention (OJ L 38, 10.2.1982). The conservation and management status within the different national legislations varies between countries (members and non-members of the EU) and depends on the degree of the local communities' interest in the conservation of the subspecies. Over the past two decades, the genus Rupicapra has been the subject of numerous genetic studies and, although Balkan chamois has been included in several of these phylogenetic studies that used both nuclear and mitochondrial markers, it remains one of the less-studied subspecies. Current knowledge on the genetic diversity and structure of the Balkan chamois population is limited and restricted to regional-local studies. Multiplex set of microsatellite loci and a partial mitochondrial control region were used to investigate the genetic structure and connectivity of Balkan chamois throughout its distribution range to support the development of management and conservation strategies. In addition, the same microsatellite set was used to determine the accuracy of existing historical data on the origin of the Biokovo population and to clarify which subspecies was present before reintroduction of Balkan chamois to Velebit Mountain. This was done with the aim to assess and document the genetic status of both the source and translocated populations. To test Balkan chamois genetic diversity and population structure, DNA from bone, dried skin and muscle tissue was extracted and successfully genotyped in 92 individuals of Balkan chamois and the partial control region was sequenced in 44 individuals. Additional 20 samples from Biokovo and 29 samples from three areas which might have served as source populations for reintroduction and possible recent recolonization (Prenj, Čvrsnica and Čabulja mountains) were genotyped. To clarify which subspecies was present before reintroduction to Velebit Mountain, four male chamois skulls originating from Velebit, collected around 25 years before the population local extinction were genotyped. The Bayesian analysis suggested that Balkan chamois are divided into 3 genetic clusters, and assigned individuals from Serbia and Bulgaria to two separate clusters, while individuals from the other countries belonged to the same cluster. Thirty new haplotypes were obtained from partial mitochondrial DNA sequences, with private haplotypes in all analysed populations and only two haplotypes shared among populations, indicating the possibility of past translocations. Both STRUCTURE and GENELAND analyses showed a clear separation of the reintroduced population on Biokovo from Prenj’ s chamois and considerable genetic similarity between the Biokovo population and the Čvrsnica–Čabulja population. This suggests that the current genetic composition of the Biokovo populations does not derive exclusively from Prenj, as suggested by the available literature and personal interviews, but also from Čvrsnica and Čabulja. GENELAND analysis recognized the Balkan chamois from Prenj as a separate cluster, distinct from the populations of Čvrsnica and Čabulja. This suggests that the Neretva River and the state M17 road are geographic barriers for the species dispersal, as they form a genetic boundary. Concerning the identification of the subspecies inhabiting Velebit Mountain before the reintroducitons, according to assignment based on microsatellite loci, using both Bayesian clustering in STRUCTURE (with q values between 0.55 and 0.73) and DAPC (with individual membership probabilities of 0.99 and 1.00), Alpine subspecies showed an higher likelihood. The subspecies’ genetic composition presented in this doctoral thesis provides the necessary starting point for assessing the conservation status of Balkan chamois and allows the development of strategies necessary for its sustainable management. The use of molecular markers, in this case microsatellites and mitochondrial DNA, provided important information on the genetic diversity and evolutionary history of Balkan chamois populations.